We have been investigating the details of a high resolution DNA structure of [d(G3T4G3)]2 which was determined by Nuclear Magnetic Resonance Spectroscopy (NMR). Using MidasPlus, and other programs, we arrived at a three-dimensional structure for this unusual DNA. Extensive molecular dynamics (MD) were performed using AMBER and the Particle Mesh Ewald (PME) summation method for dealing with long-range electrostatic charges. The "movie" program, "DISPLAY", has been used extensively to view these MD simulations, while programs such as NOESHOW have been used to discern regions where the mlecule is best fitting the NMR data. In the next step, this structure will serve as a basis for DOCK calculations aimed at identifying ligands which can recognize it. In addition, we are continuing studies on DNA-binding peptide-based ligand. In these studies the binding mode is being explored, and modifications are being tested to evaluate ways to improve sequence specificity in binding. Many of the same techniques are used for this project.